forked from mirrors/nixpkgs
215 lines
7.7 KiB
Nix
215 lines
7.7 KiB
Nix
{ nixpkgs
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, withDoc ? false
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}:
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let
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inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages_8_x;
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# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
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python = nixpkgs.python2.override {
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packageOverrides = self: super: {
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cypari2 = super.cypari2.override { inherit pari; };
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cysignals = super.cysignals.override { inherit pari; };
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cvxopt = super.cvxopt.override { inherit glpk; };
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# python packages that appear unmaintained and were not accepted into the nixpkgs
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# tree because of that. These packages are only dependencies of the more-or-less
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# deprecated sagenb. However sagenb is still a default dependency and the doctests
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# depend on it.
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# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
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flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
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flask-openid = self.callPackage ./flask-openid.nix {};
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python-openid = self.callPackage ./python-openid.nix {};
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pybrial = self.callPackage ./pybrial.nix {};
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint ecl pari glpk eclib ntl arb;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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linbox = nixpkgs.linbox.override { withSage = true; };
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};
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sagenb = self.callPackage ./sagenb.nix {
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mathjax = nodePackages_8_x.mathjax;
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};
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sagedoc = self.callPackage ./sagedoc.nix {
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inherit sage-src;
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};
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env-locations = self.callPackage ./env-locations.nix {
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inherit pari_data ecl pari;
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inherit singular;
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three = nodePackages_8_x.three;
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mathjax = nodePackages_8_x.mathjax;
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};
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sage-env = self.callPackage ./sage-env.nix {
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inherit sage-src python rWrapper openblas-cblas-pc glpk ecl singular eclib pari palp flint pynac pythonEnv giac ntl;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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};
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sage-with-env = self.callPackage ./sage-with-env.nix {
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inherit pari eclib pythonEnv ntl;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular giac;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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three = nodePackages_8_x.three;
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};
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sage = self.callPackage ./sage.nix { };
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sage-wrapper = self.callPackage ./sage-wrapper.nix {
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inherit sage-src withDoc;
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};
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};
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};
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openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
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openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
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openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
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sage-src = callPackage ./sage-src.nix {};
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pythonRuntimeDeps = with python.pkgs; [
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sagelib
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pybrial
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sagenb
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cvxopt
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networkx
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service-identity
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psutil
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sympy
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fpylll
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matplotlib
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scipy
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ipywidgets
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rpy2
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sphinx
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typing
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pillow
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];
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pythonEnv = python.buildEnv.override {
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extraLibs = pythonRuntimeDeps;
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ignoreCollisions = true;
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} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
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# needs to be rWrapper, standard "R" doesn't include default packages
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rWrapper = nixpkgs.rWrapper.override {
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# https://trac.sagemath.org/ticket/25674
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R = nixpkgs.R.overrideAttrs (attrs: rec {
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name = "R-3.4.4";
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src = fetchurl {
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url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
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sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
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};
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});
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};
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# https://trac.sagemath.org/ticket/25532
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ntl = nixpkgs.ntl.overrideAttrs (oldAttrs: rec {
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name = "ntl-10.5.0";
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sourceRoot = "${name}/src";
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src = fetchurl {
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url = "http://www.shoup.net/ntl/${name}.tar.gz";
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sha256 = "1lmldaldgfr2b2a6585m3np5ds8bq1bis2s1ajycjm49vp4kc2xr";
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};
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});
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giac = nixpkgs.giac.override { inherit ntl; };
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arb = nixpkgs.arb.override { inherit flint; };
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# update causes issues
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# https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
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# https://trac.sagemath.org/ticket/24735
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singular = (nixpkgs.singular.override { inherit ntl flint; }).overrideAttrs (oldAttrs: {
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name = "singular-4.1.0p3";
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src = fetchurl {
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url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz";
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sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4";
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};
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});
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# *not* to confuse with the python package "pynac"
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# https://trac.sagemath.org/ticket/24838 (depends on arb update)
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pynac = nixpkgs.pynac.override { inherit singular flint; };
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eclib = nixpkgs.eclib.override { inherit pari ntl; };
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# With openblas (64 bit), the tests fail the same way as when sage is build with
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# openblas instead of openblasCompat. Apparently other packages somehow use flints
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# blas when it is available. Alternative would be to override flint to use
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# openblasCompat.
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flint = nixpkgs.flint.override { withBlas = false; inherit ntl; };
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# Multiple palp dimensions need to be available and sage expects them all to be
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# in the same folder.
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palp = symlinkJoin {
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name = "palp-${nixpkgs.palp.version}";
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paths = [
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(nixpkgs.palp.override { dimensions = 4; doSymlink = false; })
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(nixpkgs.palp.override { dimensions = 5; doSymlink = false; })
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(nixpkgs.palp.override { dimensions = 6; doSymlink = true; })
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(nixpkgs.palp.override { dimensions = 11; doSymlink = false; })
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];
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};
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# Sage expects those in the same directory.
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pari_data = symlinkJoin {
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name = "pari_data";
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paths = with nixpkgs; [
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pari-galdata
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pari-seadata-small
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];
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};
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# https://trac.sagemath.org/ticket/22191
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ecl = nixpkgs.ecl_16_1_2;
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# sage currently uses an unreleased version of pari
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pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec {
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version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix`
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src = fetchurl {
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url = "mirror://sageupstream/pari/pari-${version}.tar.gz";
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sha256 = "19gbsm8jqq3hraanbmsvzkbh88iwlqbckzbnga3y76r7k42akn7m";
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};
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});
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# https://trac.sagemath.org/ticket/24824
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glpk = nixpkgs.glpk.overrideAttrs (attrs: rec {
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version = "4.63";
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name = "glpk-${version}";
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src = fetchurl {
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url = "mirror://gnu/glpk/${name}.tar.gz";
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sha256 = "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci";
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};
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patches = (attrs.patches or []) ++ [
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# Alternatively patch sage with debians
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# https://sources.debian.org/data/main/s/sagemath/8.1-7/debian/patches/t-version-glpk-4.60-extra-hack-fixes.patch
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# The header of that debian patch contains a good description of the issue. The gist of it:
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# > If GLPK in Sage causes one error, and this is caught by Sage and recovered from, then
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# > later (because upstream GLPK does not clear the "error" flag) Sage will append
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# > all subsequent terminal output of GLPK into the error_message string but not
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# > actually forward it to the user's terminal. This breaks some doctests.
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(fetchpatch {
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name = "error_recovery.patch";
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url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/error_recovery.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
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sha256 = "0z99z9gd31apb6x5n5n26411qzx0ma3s6dnznc4x61x86bhq31qf";
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})
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# Allow setting a exact verbosity level (OFF|ERR|ON|ALL|DBG)
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(fetchpatch {
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name = "exact_verbosity.patch";
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url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/glp_exact_verbosity.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
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sha256 = "15gm5i2alqla3m463i1qq6jx6c0ns6lip7njvbhp37pgxg4s9hx8";
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})
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];
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});
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in
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python.pkgs.sage-wrapper // {
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doc = python.pkgs.sagedoc;
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lib = python.pkgs.sagelib;
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}
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